PDB Short entry for 3DNF HEADER OXIDOREDUCTASE 02-JUL-08 3DNF TITLE STRUCTURE OF (E)-4-HYDROXY-3-METHYL-BUT-2-ENYL DIPHOSPHATE REDUCTASE, TITLE 2 THE TERMINAL ENZYME OF THE NON-MEVALONATE PATHWAY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ISPH, LYTB; COMPND 5 EC: 1.17.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: ISPH, LYTB, AQ_1739; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TOP 10; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PASK-AAEOLYTB KEYWDS TRILOBAL STRUCURE, OPEN ALPHA/BETA, IRON, IRON-SULFUR, ISOPRENE KEYWDS 2 BIOSYNTHESIS, METAL-BINDING, NADP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR I.REKITTKE REVDAT 3 09-SEP-20 3DNF 1 REMARK SEQADV REVDAT 2 13-JUL-11 3DNF 1 VERSN REVDAT 1 30-DEC-08 3DNF 0 JRNL AUTH I.REKITTKE,J.WIESNER,U.DEMMER,E.WARKENTIN,W.XU,K.TROSCHKE, JRNL AUTH 2 M.HINTZ,J.H.NO,E.C.DUIN,E.OLDFIELD,H.JOMAA,U.ERMLER JRNL TITL STRUCTURE OF (E)-4-HYDROXY-3-METHYL-BUT-2-ENYL DIPHOSPHATE JRNL TITL 2 REDUCTASE, THE TERMINAL ENZYME OF THE NON-MEVALONATE JRNL TITL 3 PATHWAY. JRNL REF J.AM.CHEM.SOC. 2008 JRNL REFN ESSN 1520-5126 JRNL PMID 19035630 JRNL DOI 10.1021/JA806668Q REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 77992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4120 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3498 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 222 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 561 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.70000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.195 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4610 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6243 ; 1.455 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 591 ; 5.409 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;35.011 ;24.877 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 862 ;14.371 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.739 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 714 ; 0.249 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3403 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2300 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3174 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 482 ; 0.210 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.193 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.176 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2933 ; 0.883 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4623 ; 1.329 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1880 ; 2.280 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1600 ; 3.488 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 14 A 195 REMARK 3 RESIDUE RANGE : A 2302 A 2302 REMARK 3 ORIGIN FOR THE GROUP (A): 58.7585 8.4713 26.8034 REMARK 3 T TENSOR REMARK 3 T11: -0.1706 T22: -0.1900 REMARK 3 T33: -0.2219 T12: 0.0171 REMARK 3 T13: 0.0294 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 3.3171 L22: 1.9241 REMARK 3 L33: 0.4295 L12: 0.9957 REMARK 3 L13: -0.0279 L23: -0.2346 REMARK 3 S TENSOR REMARK 3 S11: -0.0711 S12: 0.2723 S13: -0.0091 REMARK 3 S21: -0.0994 S22: 0.0985 S23: -0.1332 REMARK 3 S31: -0.0239 S32: 0.0334 S33: -0.0274 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 13 REMARK 3 RESIDUE RANGE : A 196 A 281 REMARK 3 ORIGIN FOR THE GROUP (A): 53.5263 25.3514 1.3148 REMARK 3 T TENSOR REMARK 3 T11: 0.3549 T22: 0.3567 REMARK 3 T33: -0.1699 T12: -0.0318 REMARK 3 T13: 0.0077 T23: 0.1328 REMARK 3 L TENSOR REMARK 3 L11: 9.4926 L22: 4.1512 REMARK 3 L33: 10.0421 L12: 1.5246 REMARK 3 L13: 2.5378 L23: -2.5175 REMARK 3 S TENSOR REMARK 3 S11: -0.5174 S12: 1.2309 S13: 0.7257 REMARK 3 S21: -0.8162 S22: 0.3972 S23: -0.0438 REMARK 3 S31: -0.8385 S32: -0.0517 S33: 0.1202 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 14 B 195 REMARK 3 RESIDUE RANGE : B 3302 B 3302 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0543 -5.8171 31.3510 REMARK 3 T TENSOR REMARK 3 T11: -0.1788 T22: -0.1798 REMARK 3 T33: -0.1835 T12: 0.0139 REMARK 3 T13: -0.0015 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.6317 L22: 1.4753 REMARK 3 L33: 0.3800 L12: 1.4142 REMARK 3 L13: -0.5166 L23: -0.4234 REMARK 3 S TENSOR REMARK 3 S11: -0.0633 S12: 0.1276 S13: 0.0238 REMARK 3 S21: -0.0593 S22: 0.0801 S23: -0.0257 REMARK 3 S31: 0.0496 S32: -0.0014 S33: -0.0168 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 5 B 13 REMARK 3 RESIDUE RANGE : B 196 B 282 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7808 -31.0931 16.4116 REMARK 3 T TENSOR REMARK 3 T11: 0.2648 T22: 0.1500 REMARK 3 T33: 0.0799 T12: 0.0931 REMARK 3 T13: 0.0713 T23: -0.2018 REMARK 3 L TENSOR REMARK 3 L11: 6.9508 L22: 5.3341 REMARK 3 L33: 4.7204 L12: 0.8164 REMARK 3 L13: -1.5291 L23: 1.1667 REMARK 3 S TENSOR REMARK 3 S11: -0.1921 S12: 1.1851 S13: -1.0416 REMARK 3 S21: -0.6227 S22: 0.1669 S23: -0.4486 REMARK 3 S31: 0.4421 S32: 0.0030 S33: 0.0252 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3DNF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.983 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 9.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 3.571 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.36 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % (W/W) PEG 8000, 0,1 M TRIS-HCL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 43.88000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 CYS A 282 REMARK 465 GLU A 283 REMARK 465 GLY A 284 REMARK 465 GLN A 285 REMARK 465 LEU A 286 REMARK 465 VAL A 287 REMARK 465 SER A 288 REMARK 465 SER A 289 REMARK 465 ARG A 290 REMARK 465 SER A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 465 GLU B 283 REMARK 465 GLY B 284 REMARK 465 GLN B 285 REMARK 465 LEU B 286 REMARK 465 VAL B 287 REMARK 465 SER B 288 REMARK 465 SER B 289 REMARK 465 ARG B 290 REMARK 465 SER B 291 REMARK 465 HIS B 292 REMARK 465 HIS B 293 REMARK 465 HIS B 294 REMARK 465 HIS B 295 REMARK 465 HIS B 296 REMARK 465 HIS B 297 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 3873 O HOH B 4052 2.03 REMARK 500 O HOH B 3898 O HOH B 4023 2.07 REMARK 500 O HOH B 3891 O HOH B 4107 2.11 REMARK 500 OE1 GLU B 104 O HOH B 4136 2.11 REMARK 500 OD1 ASN B 48 O HOH B 4175 2.15 REMARK 500 OE1 GLN B 59 O HOH B 4176 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 237 CB ASN A 237 CG 0.295 REMARK 500 ASN A 237 CG ASN A 237 OD1 0.201 REMARK 500 GLU A 246 C GLU A 246 O 0.124 REMARK 500 ASP B 211 CG ASP B 211 OD2 0.159 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 43 103.65 -163.77 REMARK 500 LEU A 247 101.83 -51.84 REMARK 500 ASN B 237 40.37 -85.92 REMARK 500 LEU B 247 104.91 -58.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A2302 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 F3S A2302 S2 100.4 REMARK 620 3 F3S A2302 S3 106.5 106.5 REMARK 620 4 F3S A2302 S4 97.5 133.3 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A2302 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 96 SG REMARK 620 2 F3S A2302 S1 108.3 REMARK 620 3 F3S A2302 S3 116.0 106.4 REMARK 620 4 F3S A2302 S4 111.1 113.2 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A2302 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 193 SG REMARK 620 2 F3S A2302 S1 108.8 REMARK 620 3 F3S A2302 S2 102.0 118.4 REMARK 620 4 F3S A2302 S3 127.3 103.5 97.6 REMARK 620 5 CYS A 193 SG 40.9 109.9 127.7 89.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S B3302 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 13 SG REMARK 620 2 F3S B3302 S2 99.9 REMARK 620 3 F3S B3302 S3 102.0 106.2 REMARK 620 4 F3S B3302 S4 97.5 138.5 106.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S B3302 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 96 SG REMARK 620 2 F3S B3302 S1 116.1 REMARK 620 3 F3S B3302 S3 113.4 104.5 REMARK 620 4 F3S B3302 S4 107.8 114.8 99.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S B3302 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 193 SG REMARK 620 2 F3S B3302 S1 107.2 REMARK 620 3 F3S B3302 S2 114.9 118.4 REMARK 620 4 F3S B3302 S3 111.8 104.9 98.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 2302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S B 3302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3731 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 3732 DBREF 3DNF A 1 289 UNP O67625 ISPH_AQUAE 1 289 DBREF 3DNF B 1 289 UNP O67625 ISPH_AQUAE 1 289 SEQADV 3DNF ARG A 290 UNP O67625 EXPRESSION TAG SEQADV 3DNF SER A 291 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS A 292 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS A 293 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS A 294 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS A 295 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS A 296 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS A 297 UNP O67625 EXPRESSION TAG SEQADV 3DNF ARG B 290 UNP O67625 EXPRESSION TAG SEQADV 3DNF SER B 291 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS B 292 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS B 293 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS B 294 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS B 295 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS B 296 UNP O67625 EXPRESSION TAG SEQADV 3DNF HIS B 297 UNP O67625 EXPRESSION TAG SEQRES 1 A 297 MET VAL ASP ILE ILE ILE ALA GLU HIS ALA GLY PHE CYS SEQRES 2 A 297 PHE GLY VAL LYS ARG ALA VAL LYS LEU ALA GLU GLU SER SEQRES 3 A 297 LEU LYS GLU SER GLN GLY LYS VAL TYR THR LEU GLY PRO SEQRES 4 A 297 ILE ILE HIS ASN PRO GLN GLU VAL ASN ARG LEU LYS ASN SEQRES 5 A 297 LEU GLY VAL PHE PRO SER GLN GLY GLU GLU PHE LYS GLU SEQRES 6 A 297 GLY ASP THR VAL ILE ILE ARG SER HIS GLY ILE PRO PRO SEQRES 7 A 297 GLU LYS GLU GLU ALA LEU ARG LYS LYS GLY LEU LYS VAL SEQRES 8 A 297 ILE ASP ALA THR CYS PRO TYR VAL LYS ALA VAL HIS GLU SEQRES 9 A 297 ALA VAL CYS GLN LEU THR ARG GLU GLY TYR PHE VAL VAL SEQRES 10 A 297 LEU VAL GLY GLU LYS ASN HIS PRO GLU VAL ILE GLY THR SEQRES 11 A 297 LEU GLY TYR LEU ARG ALA CYS ASN GLY LYS GLY ILE VAL SEQRES 12 A 297 VAL GLU THR LEU GLU ASP ILE GLY GLU ALA LEU LYS HIS SEQRES 13 A 297 GLU ARG VAL GLY ILE VAL ALA GLN THR THR GLN ASN GLU SEQRES 14 A 297 GLU PHE PHE LYS GLU VAL VAL GLY GLU ILE ALA LEU TRP SEQRES 15 A 297 VAL LYS GLU VAL LYS VAL ILE ASN THR ILE CYS ASN ALA SEQRES 16 A 297 THR SER LEU ARG GLN GLU SER VAL LYS LYS LEU ALA PRO SEQRES 17 A 297 GLU VAL ASP VAL MET ILE ILE ILE GLY GLY LYS ASN SER SEQRES 18 A 297 GLY ASN THR ARG ARG LEU TYR TYR ILE SER LYS GLU LEU SEQRES 19 A 297 ASN PRO ASN THR TYR HIS ILE GLU THR ALA GLU GLU LEU SEQRES 20 A 297 GLN PRO GLU TRP PHE ARG GLY VAL LYS ARG VAL GLY ILE SEQRES 21 A 297 SER ALA GLY ALA SER THR PRO ASP TRP ILE ILE GLU GLN SEQRES 22 A 297 VAL LYS SER ARG ILE GLN GLU ILE CYS GLU GLY GLN LEU SEQRES 23 A 297 VAL SER SER ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 297 MET VAL ASP ILE ILE ILE ALA GLU HIS ALA GLY PHE CYS SEQRES 2 B 297 PHE GLY VAL LYS ARG ALA VAL LYS LEU ALA GLU GLU SER SEQRES 3 B 297 LEU LYS GLU SER GLN GLY LYS VAL TYR THR LEU GLY PRO SEQRES 4 B 297 ILE ILE HIS ASN PRO GLN GLU VAL ASN ARG LEU LYS ASN SEQRES 5 B 297 LEU GLY VAL PHE PRO SER GLN GLY GLU GLU PHE LYS GLU SEQRES 6 B 297 GLY ASP THR VAL ILE ILE ARG SER HIS GLY ILE PRO PRO SEQRES 7 B 297 GLU LYS GLU GLU ALA LEU ARG LYS LYS GLY LEU LYS VAL SEQRES 8 B 297 ILE ASP ALA THR CYS PRO TYR VAL LYS ALA VAL HIS GLU SEQRES 9 B 297 ALA VAL CYS GLN LEU THR ARG GLU GLY TYR PHE VAL VAL SEQRES 10 B 297 LEU VAL GLY GLU LYS ASN HIS PRO GLU VAL ILE GLY THR SEQRES 11 B 297 LEU GLY TYR LEU ARG ALA CYS ASN GLY LYS GLY ILE VAL SEQRES 12 B 297 VAL GLU THR LEU GLU ASP ILE GLY GLU ALA LEU LYS HIS SEQRES 13 B 297 GLU ARG VAL GLY ILE VAL ALA GLN THR THR GLN ASN GLU SEQRES 14 B 297 GLU PHE PHE LYS GLU VAL VAL GLY GLU ILE ALA LEU TRP SEQRES 15 B 297 VAL LYS GLU VAL LYS VAL ILE ASN THR ILE CYS ASN ALA SEQRES 16 B 297 THR SER LEU ARG GLN GLU SER VAL LYS LYS LEU ALA PRO SEQRES 17 B 297 GLU VAL ASP VAL MET ILE ILE ILE GLY GLY LYS ASN SER SEQRES 18 B 297 GLY ASN THR ARG ARG LEU TYR TYR ILE SER LYS GLU LEU SEQRES 19 B 297 ASN PRO ASN THR TYR HIS ILE GLU THR ALA GLU GLU LEU SEQRES 20 B 297 GLN PRO GLU TRP PHE ARG GLY VAL LYS ARG VAL GLY ILE SEQRES 21 B 297 SER ALA GLY ALA SER THR PRO ASP TRP ILE ILE GLU GLN SEQRES 22 B 297 VAL LYS SER ARG ILE GLN GLU ILE CYS GLU GLY GLN LEU SEQRES 23 B 297 VAL SER SER ARG SER HIS HIS HIS HIS HIS HIS HET F3S A2302 7 HET GOL A3731 6 HET F3S B3302 7 HET GOL B3732 6 HETNAM F3S FE3-S4 CLUSTER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 F3S 2(FE3 S4) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *561(H2 O) HELIX 1 1 CYS A 13 LEU A 27 1 15 HELIX 2 2 ASN A 43 GLY A 54 1 12 HELIX 3 3 PRO A 77 LYS A 87 1 11 HELIX 4 4 CYS A 96 GLU A 112 1 17 HELIX 5 5 HIS A 124 CYS A 137 1 14 HELIX 6 6 THR A 146 HIS A 156 5 11 HELIX 7 7 ASN A 168 VAL A 183 1 16 HELIX 8 8 ASN A 194 ALA A 207 1 14 HELIX 9 9 PRO A 208 VAL A 210 5 3 HELIX 10 10 SER A 221 ASN A 235 1 15 HELIX 11 11 THR A 243 LEU A 247 5 5 HELIX 12 12 GLN A 248 ARG A 253 5 6 HELIX 13 13 PRO A 267 ILE A 281 1 15 HELIX 14 14 CYS B 13 LEU B 27 1 15 HELIX 15 15 ASN B 43 GLY B 54 1 12 HELIX 16 16 PRO B 77 LYS B 87 1 11 HELIX 17 17 CYS B 96 GLU B 112 1 17 HELIX 18 18 HIS B 124 CYS B 137 1 14 HELIX 19 19 THR B 146 HIS B 156 5 11 HELIX 20 20 ASN B 168 VAL B 183 1 16 HELIX 21 21 ASN B 194 ALA B 207 1 14 HELIX 22 22 PRO B 208 VAL B 210 5 3 HELIX 23 23 SER B 221 ASN B 235 1 15 HELIX 24 24 THR B 243 LEU B 247 5 5 HELIX 25 25 GLN B 248 ARG B 253 5 6 HELIX 26 26 PRO B 267 CYS B 282 1 16 SHEET 1 A 4 ASP A 3 ILE A 6 0 SHEET 2 A 4 ARG A 257 ALA A 262 1 O VAL A 258 N ILE A 5 SHEET 3 A 4 VAL A 212 ILE A 216 1 N ILE A 214 O GLY A 259 SHEET 4 A 4 THR A 238 ILE A 241 1 O TYR A 239 N MET A 213 SHEET 1 B 4 VAL A 55 PRO A 57 0 SHEET 2 B 4 VAL A 34 THR A 36 1 N VAL A 34 O PHE A 56 SHEET 3 B 4 THR A 68 ILE A 71 1 O THR A 68 N TYR A 35 SHEET 4 B 4 LYS A 90 ASP A 93 1 O ILE A 92 N VAL A 69 SHEET 1 C 8 GLY A 141 VAL A 144 0 SHEET 2 C 8 PHE A 115 VAL A 119 1 N LEU A 118 O VAL A 144 SHEET 3 C 8 ARG A 158 ALA A 163 1 O GLY A 160 N VAL A 117 SHEET 4 C 8 GLU A 185 ILE A 189 1 O LYS A 187 N ILE A 161 SHEET 5 C 8 GLU B 185 ILE B 189 -1 O VAL B 188 N VAL A 186 SHEET 6 C 8 ARG B 158 ALA B 163 1 N ILE B 161 O LYS B 187 SHEET 7 C 8 PHE B 115 VAL B 119 1 N VAL B 117 O GLY B 160 SHEET 8 C 8 GLY B 141 VAL B 144 1 O ILE B 142 N LEU B 118 SHEET 1 D 4 ASP B 3 ILE B 6 0 SHEET 2 D 4 ARG B 257 ALA B 262 1 O VAL B 258 N ILE B 5 SHEET 3 D 4 VAL B 212 ILE B 216 1 N VAL B 212 O GLY B 259 SHEET 4 D 4 THR B 238 ILE B 241 1 O ILE B 241 N ILE B 215 SHEET 1 E 4 VAL B 55 PRO B 57 0 SHEET 2 E 4 VAL B 34 THR B 36 1 N VAL B 34 O PHE B 56 SHEET 3 E 4 THR B 68 ILE B 71 1 O THR B 68 N TYR B 35 SHEET 4 E 4 LYS B 90 ASP B 93 1 O ILE B 92 N VAL B 69 SSBOND 1 CYS A 107 CYS A 137 1555 1555 2.92 SSBOND 2 CYS B 107 CYS B 137 1555 1555 2.07 LINK SG CYS A 13 FE4 F3S A2302 1555 1555 2.52 LINK SG CYS A 96 FE3 F3S A2302 1555 1555 2.31 LINK SG ACYS A 193 FE1 F3S A2302 1555 1555 2.40 LINK SG CCYS A 193 FE1 F3S A2302 1555 1555 2.52 LINK SG CYS B 13 FE4 F3S B3302 1555 1555 2.54 LINK SG CYS B 96 FE3 F3S B3302 1555 1555 2.17 LINK SG CYS B 193 FE1 F3S B3302 1555 1555 2.35 SITE 1 AC1 7 CYS A 13 GLY A 15 CYS A 96 TYR A 98 SITE 2 AC1 7 THR A 165 CYS A 193 ALA A 195 SITE 1 AC2 6 CYS B 13 GLY B 15 CYS B 96 THR B 165 SITE 2 AC2 6 CYS B 193 ALA B 195 SITE 1 AC3 5 GLY A 113 LYS A 140 HIS A 156 GLU A 157 SITE 2 AC3 5 ARG A 158 SITE 1 AC4 5 GLY B 113 LYS B 140 HIS B 156 GLU B 157 SITE 2 AC4 5 ARG B 158 CRYST1 60.370 87.760 72.400 90.00 95.13 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016565 0.000000 0.001487 0.00000 SCALE2 0.000000 0.011395 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013868 0.00000